SRX3981855
GSM3106393: ChIP-seq from A549 (ENCLB272EBJ); Homo sapiens; ChIP-Seq

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC3

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

sample_type
cell line
cell line
A549
sex
male
dev_stage
adult
age
58 year
donor ID
ENCDO000AAZ
lab
Tim Reddy, Duke
treatments
treatment_term_id: CHEBI:41879; treatment_term_name: dexamethasone; treatment_type: chemical; duration: 7; duration_units: hour;

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
general protocol: https://www.encodeproject.org/documents/e21fb833-cd54-4c37-a3b6-440732909433/@@download/attachment/01_ChIP_DEX_Harvest_Reddy_GGR.pdf treatment protocol: https://www.encodeproject.org/documents/1bca5eae-b9ce-4df0-b401-612924dc53a4/@@download/attachment/03_KAPA_Hyper_Prep_Kit_KR0961-TDSv2.15_final_24%20rxn_Reddy_GGR.pdf general protocol: https://www.encodeproject.org/documents/0d841e8a-a32d-416e-8f99-9db162bd09be/@@download/attachment/03_notes_Reddy_GGR.pdf treatment protocol: https://www.encodeproject.org/documents/ce21a05f-b788-4f2b-83e2-47213283829d/@@download/attachment/ChIP_DEX_treatment.pdf extraction protocol: https://www.encodeproject.org/documents/4ac7e9ce-4a92-42da-a1ab-299d4205eb96/@@download/attachment/02_ChIP_shearing_IP_reverse_v.2_Reddy_GGR.pdf

Sequencing Platform

instrument_model
Illumina HiSeq 2500

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
21270807
Reads aligned (%)
98.9
Duplicates removed (%)
5.9
Number of peaks
17847 (qval < 1E-05)

hg19

Number of total reads
21270807
Reads aligned (%)
98.5
Duplicates removed (%)
6.5
Number of peaks
17879 (qval < 1E-05)

Base call quality data from DBCLS SRA